Protein Folding Under Confinement

Abstract

The study of proteins near an interface is relevant to understanding their in vivo behavior inside biological bodies. Previous studies have shown that the folding process of the protein can be affected by nearby interfaces. Here we perform Monte Carlo simulations of a coarse-grained model of proteins, in explicit water, near a flat hydrophobic interface. Due to the periodic boundary conditions of the system, the interface effectively confines the system in one direction as in a slit pore. We consider four different proteins, two with 60 and two with 100 amino acids (aa), and study their folding in bulk and confined water by calculating the system's free energy. We observe that the 60 aa-long proteins spontaneously fold in bulk and confined water. On the other hand, the 100 aa-long proteins are stable in bulk but unable to refold within our simulation time. For the two shortest proteins, we test the effect of confinement. We observe the absorption of the folded proteins on the hydrophobic interface with no drastic changes in their folding process. We interpret this weak effect as a consequence of the large separation between the slit pore surfaces